bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Title
Human pancreatic β cell lncRNAs control cell-specific regulatory networks
Authors
Ildem Akerman1,2,3, Zhidong Tu 4, Anthony Beucher1, Delphine M.Y. Rolando1, Claire
Sauty-Colace5, Marion Benazra5, Nikolina Nakic1, Jialiang Yang4, Huan Wang4,
Lorenzo Pasquali3,6, Ignasi Moran1, Javier Garcia-Hurtado2,3, Natalia Castro2,3,
Roser Gonzalez-Franco1, Andrew Stewart7, Caroline Bonner8, Lorenzo Piemonti9,
Thierry Berney10, Leif Groop11, Julie Kerr-Conte8, Francois Pattou8, Carmen
Argmann4, Eric Schadt4, Philippe Ravassard5, Jorge Ferrer1,2,3
Affiliations
1. Section of Epigenomics and Disease, Department of Medicine, Imperial College
London, London W12 0NN, United Kingdom
2. Genomic Programming of Beta Cells Laboratory, Institut d’Investigacions
Biomediques August Pi I Sunyer (IDIBAPS), Barcelona 08036, Spain
3. Centro de Investigación Biomédica en Red de Diabetes y Enfermedades
Metabólicas Asociadas (CIBERDEM), Madrid 28029, Spain.
4. Department of Genetics and Genomic Science, Icahn School of Medicine at
Mount Sinai, New York 10029, USA.
5. Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du cerveau et
de la moelle (ICM) – Hôpital Pitié-Salpêtrière, Boulevard de l’Hôpital, Paris F-75013,
France.
6. Germans Trias i Pujol University Hospital and Research Institute and Josep
Carreras Leukaemia Research Institute, Badalona 08916, Spain
1
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
7. Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount
Sinai, New York 10029, USA
8. European Genomic Institute for Diabetes, Inserm UMR 1190, Lille 59800, France
9. Diabetes research institute (HSR-DRI), San Raffaele Scientific Institute, Milano
20132, Italy
10. Cell Isolation and Transplantation Center, University of Geneva, 1211 Geneva-4,
Switzerland
11. Department of Clinical Sciences, Lund University Diabetes Centre, Lund
University, Lund 205 02, Sweden.
Contact Information
Lead contact and corresponding author: [email protected]
2
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Summary
Recent studies have uncovered thousands of long non-coding RNAs (lncRNAs) in
human pancreatic β cells. β cell lncRNAs are often cell type-specific, and exhibit
dynamic regulation during differentiation or upon changing glucose concentrations.
Although these features hint at a role of lncRNAs in β cell gene regulation and
diabetes, the function of β cell lncRNAs remains largely unknown. In this study, we
investigated the function of β cell-specific lncRNAs and transcription factors using
transcript knockdowns and co-expression network analysis. This revealed lncRNAs
that function in concert with transcription factors to regulate β cell-specific
transcriptional networks. We further demonstrate that lncRNA PLUTO affects local
three-dimensional chromatin structure and transcription of PDX1, encoding a key β
cell transcription factor, and that both PLUTO and PDX1 are downregulated in islets
from donors with type 2 diabetes or impaired glucose tolerance. These results
implicate lncRNAs in the regulation of β cell-specific transcription factor networks.
3
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Introduction
Transcriptome surveys have uncovered tens of thousands of mammalian transcripts
longer than 200 nucleotides that have low protein-coding potential (Carninci et al.,
2005; Derrien et al., 2012; Guttman et al., 2009). A small fraction of these long noncoding RNAs (lncRNAs) have been shown to control gene expression by modulating
chromosomal structure, transcription, splicing, mRNA transport, stability or
translation (Carrieri et al., 2012; Chen and Carmichael, 2009; Gong and Maquat,
2011; Lai et al., 2013; Luco and Misteli, 2011; Willingham et al., 2005; Yao et al.,
2010). Specific lncRNAs have thus been implicated in various key processes,
including random X chromosome inactivation, imprinting, the cell cycle,
organogenesis, differentiation, pluripotency, and cancer progression (Guttman et al.,
2011; Huarte et al., 2010; Hung et al., 2011; Klattenhoff et al., 2013; Kretz et al.,
2013; Penny et al., 1996; Schmitt and Chang, 2013; Sleutels et al., 2002; Ulitsky et
al., 2011). Despite these wide ranging biological roles, the fraction of lncRNAs that is
genuinely functional, and the true impact of lncRNAs in human biology and disease
remains poorly understood.
Pancreatic β cells regulate glucose homeostasis by secreting the insulin, and play a
central role in the pathogenesis of major forms of diabetes mellitus. Recently, more
than 1100 lncRNAs were identified in human pancreatic islets and purified β cells
(Moran et al., 2012), as well as in mouse pancreatic islet cells (Benner et al., 2014;
Ku et al., 2012; Moran et al., 2012). A large fraction of human β cell lncRNAs are
cell-specific, and several are known to be activated during β cell differentiation
(Moran et al., 2012). This cellular specificity has also been noted for lncRNAs in
other cell types (Cabili et al., 2011; Derrien et al., 2012), and points to the possibility
4
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
that lncRNAs may regulate genetic programs important for lineage-specific
differentiation or specialized cellular functions. Further, several β cell lncRNAs were
shown to be regulated by extracellular glucose concentrations, suggesting a
potential role of lncRNAs in the functional adaptation of β cells to increased insulin
secretory demands (Moran et al., 2012). Some islet lncRNAs map to loci that contain
polygenic or Mendelian defects associated with human diabetes, while selected
lncRNAs show deregulation in islets from organ donors with human type 2 diabetes
(T2D) (Fadista et al., 2014; Moran et al., 2012). Collectively, these properties define
a newly identified class of candidate regulators of β cell differentiation and function,
with potential implications for human diabetes mellitus. However, the true relevance
of β cell lncRNAs depends on whether they elicit a physiological function in human β
cells, which remains to be addressed systematically.
In the current study, we have focused on a set of lncRNAs that show restricted
expression in human pancreatic β cells, and have tested the hypothesis that they
regulate β cell gene expression. Our studies have uncovered a regulatory network in
which lineage-specific lncRNAs and transcription factors (TFs) control common
genes. Furthermore, we show that lncRNAs frequently regulate genes associated
with clusters of islet enhancers, which have previously been shown to be the primary
functional targets of islet-specific TFs. Detailed analysis of a specific lncRNA named
PLUTO controls PDX1, a master regulator of pancreas development and β cell
differentiation, and thereby modulates the PDX1-dependent transcriptional program.
Finally, we show that PLUTO and PDX1 are downregulated in islets from organ
donors with type 2 diabetes or impaired glucose tolerance, suggesting a potential
role in human diabetes.
5
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Results
Human β cell lncRNA knockdowns cause profound transcriptional phenotypes
To directly test the regulatory function of pancreatic β cell lncRNAs, we carried out
loss of function experiments in a glucose-responsive human islet β cell line, EndoCβH1 (Ravassard et al., 2011). We chose a human model because only some human
lncRNAs are evolutionary conserved (Derrien et al., 2012; Moran et al., 2012;
Okazaki et al., 2002; Pang et al., 2006), and we perturbed the function of lncRNAs
through RNAi-based transcript knockdowns rather than genomic deletions because
deletions could potentially disrupt cis-regulatory elements. We thus designed
lentiviral vectors that contain RNA Polymerase II-transcribed artificial miRNAs
(hereafter referred to as amiRNA) with perfect homology to the target sequence so
as to elicit target cleavage. The amiRNAs contain an artificial stem sequence
targeting our lncRNA of choice as well as flanking and loop sequences from an
endogenous miRNA to allow their processing as pre-miRNA by the RNAi pathway
(Figure S1A). As a reference, we used the same strategy to knockdown TFs that are
well known to regulate gene expression in pancreatic islets, as well as five different
non-targeting amiRNA sequences as controls.
The lncRNAs selected for knockdown were derived from a shortlist of 25 lncRNAs
that showed (i) a markedly enriched expression in human islets and FACS-purified β
cells relative to exocrine pancreas and a panel of non-pancreatic tissues, (ii)
expression in the EndoC-βH1 β cell line, and (iii) a chromatin profile in human islets
that was consistent with an active promoter (Figure S1C-D). Of these 25 lncRNAs,
12 were shortlisted because they were near a protein-coding gene that has an
important function in β cells. The lncRNAs had variable subcellular enrichment
6
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
patterns (Figure S1B) and eight of the 12 lncRNAs had detectable transcripts in
orthologous or syntenic mouse regions (Table S1)(Moran et al., 2012). We then
screened four amiRNA sequences for each of the 12 lncRNAs and identified two
efficient (>50% knockdown) amiRNAs for 7 lncRNAs, and one efficient amiRNA
sequence for the other five lncRNAs (Figure S1E). Two efficient amiRNAs were also
obtained for five essential islet TFs (HNF1A, GLIS3, MAFB, NKX2.2, PDX1). We
thus transduced EndoC-βH1 cells with lentiviruses expressing each amiRNA. This
was done in duplicate, or in triplicate for lncRNAs that only had one efficient
amiRNA. 80 hrs post-transduction, RNA was harvested and hybridized to
oligonucleotide microarrays (Figure 1A). For each target gene, we combined
expression data from all knockdowns and compared them to the control
transductions with five different control amiRNAs to identify genes that were
differentially expressed at a significance level of p<10-3 (ANOVA) (Figure 1B).
As expected, the knockdown of islet TFs consistently produced transcriptional
phenotypes (Figure 1B). Remarkably, the knockdown of 9 of the 12 islet lncRNAs
also caused transcriptional changes (Figure 1B, S1F). A more detailed analysis
showed that some of the lncRNAs that presented knockdown phenotypes had visible
effects on a neighboring gene, suggesting a possible cis-regulatory mechanism,
although other such lncRNAs did not appear to affect neighboring genes, and may
thus function through trans-regulatory mechanisms (Figure 1E and S1G). These
loss of function experiments with selected lncRNAs therefore suggested that
lncRNAs can regulate the expression of pancreatic β cell genes.
Gene silencing using the RNAi pathway can theoretically lead to nonspecific gene
deregulation. In our experimental model, a significant nonspecific result would occur
7
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
if two unrelated amiRNAs elicited changes in a common set of genes that were not
observed in the panel of control non-targeting amiRNAs. To assess the likelihood
that two unrelated amiRNA sequences elicit such an effect, we studied the 5 sets of
control (non-targeting) amiRNAs, compared all 10 possible combinations of 2 vs. 3
control amiRNAs, and determined the number of differentially expressed genes
(Figure 1C). Likewise, for each TF or lncRNA which had two valid amiRNAs, we
compared the two target-specific amiRNAs against all possible combinations of three
control amiRNAs (Figure 1C). As seen in Figure 1D, control vs. control
comparisons generated a median of 16 (IQR=15-22) differentially expressed genes,
whereas all five TFs and six of the seven lncRNA knockdowns led to a significantly
higher number of differentially expressed genes (Mann-Whitney test p<10-4 for all
lncRNA/TF vs. control comparisons except HI-LNC75, p=0.004, and HI-LNC76,
p>0.5). These results show that the observed phenotypes are unlikely to be caused
by unspecific effects of amiRNAs, and indicate that the sequence-specific inhibition
of selected islet lncRNAs can result in transcriptional changes comparable in
magnitude to the inhibition of well established islet transcriptional regulators.
The primary function of β cells is to synthesize and secrete insulin in response to
changes in glucose concentrations. Amongst the genes that showed functional
dependence on lncRNAs we identified numerous genes that are known to regulate
transcription or secretion in β cells, including RFX6, PDX1, CACNA1D, ATP2A3,
ROBO1 and 2, PDE8A, ATP6AP1, KCNJ15, TRPM3, ERO1LB and HADH (Figure
2A) (Anderson et al., 2011; Li et al., 2010; Louagie et al., 2008; Okamoto et al.,
2012; Smith et al., 2010; Tian et al., 2012; Varadi and Rutter, 2002; Wagner et al.,
2008; Yang et al., 2013; Zito et al., 2010). We therefore measured insulin content
and glucose-stimulated insulin secretion (GSIS) in T-antigen excised EndoC-βH3
8
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
cells after knocking down four lncRNAs that showed the strongest transcriptional
phenotypes (HI-LNC12, HI-LNC78, HI-LNC80 and HI-LNC71). Congruent with the
broad transcriptional phenotype, we observed reduced insulin content and
consequently impaired glucose-stimulated insulin secretion for HI-LNC12, HI-LNC78,
and HI-LNC71 knockdowns (Figure 2B). For HI-LNC78, a glucose-regulated islet
transcript (Moran et al, 2012) that is orthologous to mouse Tunar and zebrafish
megamind(linc-birc6) lncRNAs (Ulitsky et al., 2011), there was a reduction in GSIS after
correcting for the reduction in insulin content (p=0.002) (Figure S2A). To further
validate these effects, the same lncRNAs were downregulated using antisense
locked nucleic acids (LNATM GapmeRs, Exiqon), which also led to impaired insulin
secretion after knockdown of HI-LNC12 and HI-LNC78 (Figure S2B). Taken
together, lncRNA knockdown studies identified lncRNAs that modulate gene
expression and consequently insulin secretion in a human β cell line.
Human islet lncRNAs and TFs regulate common gene expression programs
To gain insight into the expression programs that are regulated by islet-specific
lncRNAs and TFs, we compared their knockdown gene expression phenotypes. We
first assessed changes in gene expression occurring after knockdown of the different
islet TFs, and found high Pearson correlation values for all pairwise comparisons (r =
0.4-0.8, p<10-27)(Figure 3A, S3). This finding is consistent with the notion that isletspecific TFs often bind to common genomic targets and function in a combinatorial
manner (Pasquali et al., 2014; Qiu et al., 2002; Wilson et al., 2003). Interestingly, the
transcriptional changes that occurred after the inhibition of several lncRNAs
significantly correlated with those observed following inhibition of TFs (Figure 3A
and S3, see also a cluster analysis of TF and lncRNA-dependent changes in Figure
3B). Some pairwise comparisons that illustrate this finding include HI-LNC78-
9
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
dependent gene expression changes, which correlated highly with HNF1A and
MAFB dependent changes (Pearson´s r=0.87 and 0.89, respectively, p<10-71), and
HI-LNC15-dependent changes, which correlated with those occurring after
knockdown of NKX2-2 (r=0.67, p=10-32) (Figure 3C). The results from these gene
knockdown experiments therefore indicate that selected islet-specific lncRNAs and
TFs can regulate common gene expression programs.
Islet TFs and lncRNAs co-regulate genes associated with enhancer clusters
Recent studies have revealed that islet TFs regulate cell-specific transcription by
targeting clusters of enhancers, and in particular clusters with enhancers that are
bound by multiple islet TFs (Pasquali et al., 2014). Enhancer clusters share many
features with regulatory domains that have otherwise been defined as “stretch
enhancers” or “super-enhancers” (Pasquali et al., 2014; Pott and Lieb, 2015). Given
that knock-down of islet lncRNAs and TFs suggested that they regulate similar
genes, we asked if islet lncRNAs also regulate enhancer cluster-associated genes.
As expected, Gene Set Enrichment Analysis (GSEA) showed that genes with isletenriched expression, genes associated with enhancer clusters, or genes associated
with enhancers that are bound by multiple TFs were downregulated after knockdown
of all five TFs, whereas this was not observed for ten control sets of genes
expressed at similar levels (Figure 4, Figure S4A,B). Likewise, genes associated
with enhancer clusters and those showing islet-specific expression were also
enriched among genes that were downregulated after knockdown of HI-LNC12, 15,
30, 78, 80, 85 and 71 (Figure 4, Figure S4A,B). These results therefore indicate
that islet-specific TFs and lncRNAs often co-regulate genes that are associated with
enhancer clusters.
10
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
β cell lncRNAs and TFs form part of islet-specific co-expression networks.
We next used an independent experimental approach to validate the observations
that human β cell lncRNAs and TFs regulate common gene expression programs.
This involved the analysis of gene modules that show co-expression across a panel
of human islet RNA samples. Analogous approaches have been employed to reveal
sets of genes that share functional relationships (Derry et al., 2010; Kim et al., 2001;
Pandey et al., 2010; Segal et al., 2003; Stuart et al., 2003; Su et al., 2011). We
implemented this analysis using weighted gene co-expression analysis (WGCNA) of
RNA-seq profiles from 64 human pancreatic islet samples. This identified 25 major
gene modules containing >100 genes, named M1-M25, which showed highly
significant co-expression across human islet samples (Figure 5A, Table S2). We
next determined which co-expression modules contained islet lncRNAs. Rather than
using our previously defined set of lncRNAs, this analysis was performed with a set
of 2373 β cell lncRNAs that was newly annotated using ~5 billion stranded RNA-seq
reads pooled from 41 islet samples (Table S3, Figure S5A). β cell lncRNAs were
found to be enriched in seven pancreatic islet co-expression modules (M3, M7, M12,
M13, M18, M20, M21) (Figure 5B).
We next characterized the nature of these seven lncRNA-enriched co-expression
modules. Five of these (M3, M7, M12, M18, M20) were enriched in genes associated
with pancreatic islet enhancer clusters (Figure 5A-C, marked in blue). Two other
modules (M13, M21) were enriched for ubiquitously expressed genes involved in
mRNA translation and metabolic pathways (Figure S5B). Amongst the modules
enriched in lncRNAs and enhancer clusters, three (M3, M7, M18) were also enriched
in islet-specific TF genes (Figure 5D), and two of these modules (M3, M7) contained
nine of the 12 lncRNAs that had been knocked down in EndoC-βH1 cells. Module
11
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
M3, the largest of the seven lncRNA-enriched modules, featured gene ontology (GO)
terms associated with prototypical islet cell functions and contained several islet TFs
and lncRNAs (Figure 5E). In keeping with these findings, we found numerous
instances of islet lncRNAs and known cell-specific TFs that showed a tight
correlation of gene expression levels across human islet samples (Figure 5F, S5C).
These findings thus indicated that β cell-specific lncRNAs, TFs, and genes
associated with islet enhancer clusters form part of common expression programs.
Further analysis is consistent with the notion that lncRNAs play a functional role in
driving gene expression variation in the lncRNA-enriched co-expression modules.
First, the subset of lncRNAs that were shown to regulate an adjacent gene in
knockdown studies also exhibited a particular high co-regulation with the adjacent
gene across islet samples (Figure S1G). This observation was extended to define
292 lncRNAs that displayed a highly significant (p<10-7) correlation of expression
with an adjacent protein-coding gene in the panel of human islet samples, and are
thus candidate cis-regulatory lncRNAs (Table S6). Second, we analyzed all genes
that were significantly downregulated in EndoC-βH1 cells after knocking down HILNC12, 71, 78 and 80, and found that they were also enriched amongst genes in
human islet modules M3, M7 and M18, but not in size-controlled modules (Figure
S5D). In summary, co-expression analysis of native human islets corroborated the
findings observed with amiRNA-based perturbations in EndoC-βH1 cells, and
indicated that a group of islet lncRNAs and TFs form part of common transcriptional
networks that target clusters of pancreatic islet enhancers (Figure 5G).
Deregulation of β cell lncRNAs in human T2D
12
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
The identification of functional lncRNAs led us to explore whether some lncRNAs are
abnormally expressed in human T2D, and might thus be relevant to the
pathogenesis of this disease. We therefore analyzed our new set of 2373 lncRNAs in
a recently reported gene expression dataset that includes human islet samples from
donors diagnosed with T2D or impaired glucose tolerance (IGT) (Fadista et al.,
2014). Our results showed that, despite the fact that gene expression across human
islet donors is highly variable, the expression of 15 and 100 lncRNAs was
significantly altered in islets from T2D and IGT vs. non-diabetic donors, respectively
(adjusted p<0.05) (Figure S6A, see Table S7 for a complete list). This finding
suggests a potential role of functional β cell lncRNAs in driving some of the β cell
gene expression changes that are associated with T2D.
PLUTO regulates PDX1, an essential transcriptional regulator
To explore how β cell lncRNAs can regulate cell-specific transcriptional networks, we
focused on HI-LNC71, a nuclear-enriched transcript (Figure S1B) that is transcribed
from a promoter that is located ~3 kb upstream of PDX1, in an antisense orientation
(Figure S6B). PDX1 is an essential transcriptional regulator of pancreas
development and β cell function that has been implicated in genetic mechanisms
underlying Mendelian and type 2 diabetes (Ahlgren et al., 1998; Jonsson et al., 1994;
Offield et al., 1996; Stoffers et al., 1997). Based on this genomic location, we
renamed HI-LNC71 as PLUTO, for PDX1 Locus Upstream Transcript.
The potential importance of PLUTO was strengthened by the observation that
PLUTO was among the most markedly downregulated lncRNAs in islets from T2D or
IGT donors (adjusted p-value = 0.07 and 0.005, respectively, Figure 6A, S6B).
13
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Interestingly, PDX1 was also downregulated in islets from donors with T2D and IGT
(Figure 6A).
PLUTO is a multi-isoform transcript that contains five major exons that span nearly
100 kb, encompassing a cluster of enhancers that make three-dimensional (3D)
contacts with the PDX1 promoter in human islets and in EndoC-βH1 cells (Figure
6B, S6A). This observation suggested that PLUTO could affect cis-regulation of the
PDX1 gene.
To test whether PLUTO regulates PDX1, we first examined EndoC-βH1 cells after
amiRNA-mediated knockdown of PLUTO RNA, and found reduced PDX1 mRNA and
protein levels (Figure 6C). Similarly, knockdown of PLUTO RNA in dispersed
primary human islet cells caused decreased PDX1 mRNA (Figure 6D). To validate
these experiments through a complementary approach, we used CRISPR
interference (CRISPRi), which involves targeting guide RNAs (gRNAs) downstream
of a gene’s transcriptional initiation site to block its transcription. Two independent
gRNAs that targeted a region downstream of the PLUTO initiation site efficiently
reduced PLUTO RNA levels relative to non-targeting gRNAs, and in both cases this
led to decreased PDX1 mRNA expression (Figure 6E). Therefore, perturbing either
PLUTO RNA levels or its transcription leads to the same inhibitory effect on PDX1
mRNA.
The mouse Pdx1 locus also has an islet lncRNA (Pluto) that shows only limited
sequence homology with human PLUTO. Pluto is also transcribed from the opposite
strand of Pdx1, but is initiated from a promoter within the first intron of Pdx1, and like
PLUTO, spans a broad regulatory domain upstream of Pdx1 (Figure S6C).
Knockdown of Pluto RNA in the mouse β cell line MIN6 also led to decreased Pdx1
14
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
mRNA levels (Figure S6E). These experiments therefore indicated that PLUTO
regulates PDX1 mRNA in human β cell lines and primary islet cells, and an
analogous effect was observed for the mouse lncRNA ortholog.
Consistent with this regulatory relationship, PLUTO and PDX1 RNA levels are highly
correlated across islet samples (Pearson´s r=0.86, p=10-15, Figure 6F), and
knockdown of PDX1 and PLUTO in EndoC-βH1 cells resulted in the deregulation of
a shared set of genes (Figure 6G-J). Furthermore, Pluto and Pdx1 were found to be
regulated with nearly identical dynamics in response to a shift in glucose
concentration (4 to 11 mM) in mouse pancreatic islets (Figure S6D). PLUTO and
PDX1 therefore regulate a common program in pancreatic islets, and this is at least
in part explained by the fact that PLUTO regulates PDX1.
PLUTO regulates PDX1 transcription and local 3D chromatin structure
To assess the mechanisms underlying the function of PLUTO, we first examined if
PLUTO controls the stability or transcription of PDX1. Transcriptional inhibition
experiments using Actinomycin D showed no significant differences in the stability of
PDX1 mRNA upon PLUTO knockdown (Figure 7A). By contrast, intronic PDX1 RNA
was reduced upon PLUTO knockdown, suggesting that PLUTO regulates PDX1
transcription (Figure 7B).
Because PLUTO spans an enhancer cluster, we hypothesized that it could regulate
the chromatin state of active enhancers. We thus knocked down PLUTO in β cells
and measured H3K27 acetylation, as well as H3K4 mono and tri-methylation levels
at several enhancers within the cluster. Our results indicate no significant changes in
these characteristic active chromatin marks (Figure S7).
15
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
We next determined whether PLUTO affects the 3D contacts between the enhancer
cluster and the PDX1 promoter. Examination of the PDX1 locus using quantitative
chromatin conformation capture (3C) assays revealed that two far upstream
enhancers (Figure 7C) showed reduced contacts with the PDX1 promoter after
PLUTO knockdown (Figure 7D). These findings therefore show that PLUTO
regulates the transcription of PDX1, a key pancreatic β cell transcriptional regulator,
and that this is associated with its ability to promote contacts between the PDX1
promoter and its enhancer cluster (Figure 7E).
Discussion
In the current study we have tested the hypothesis that lncRNAs play a role in cellspecific gene regulation in pancreatic β cells, a cell type that is central in the
pathogenesis of human diabetes. We have thus carried out for the first time a
systematic analysis of the function of a set of human β cell-specific lncRNAs. Our
experiments revealed several examples of β cell lncRNAs in which sequencespecific perturbation causes transcriptional and functional phenotypes. We have
further shown that β cell-specific lncRNAs and TFs regulate a common
transcriptional network. Finally, we have demonstrated that β cell-specific lncRNAs
directly or indirectly participate in the regulation of human enhancer clusters, which
are the major functional targets of islet-specific transcription factors and key cisregulatory determinants of islet cell transcriptional programs (Pasquali et al., 2014).
Importantly, these conclusions are supported by concordant results from coexpression network analysis and loss of function experiments. These studies should
be interpreted in light of previous evidence indicating that a significant fraction of
lncRNAs show lineage-specific expression (Cabili et al., 2011; Derrien et al., 2012;
Goff et al., 2015; Guttman et al., 2011; Iyer et al., 2015; Moran et al., 2012; Pauli et
16
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
al., 2012). Our study extends previous findings by demonstrating a functional role of
lncRNAs in lineage-specific TF networks.
Our findings invite the question of what molecular mechanisms underlie the
regulatory effects of β cell lncRNAs. LncRNAs have been proposed to control gene
expression through diverse molecular mechanisms, including the formation of
protein-specific interactions and scaffolds, RNA-DNA or RNA-RNA hybrids, the
titration of miRNAs, and the modulation of 3D chromosomal structures (Rinn and
Chang, 2012; Wang and Chang, 2011), while some transcripts currently defined as
lncRNAs can theoretically encode for atypical small peptide sequences (Andrews
and Rothnagel, 2014). Our knockdown and co-expression analyses have identified
a subset of functional lncRNAs that appear to regulate a nearby gene, suggesting a
lncRNA-based cis-regulatory mechanism, while others are likely to exert transregulatory effects. We focused on one functional nuclear-enriched β cell lncRNA,
PLUTO, and found that its function in β cell networks is at least in part due to its
ability to elicit an effect on the transcription of its adjacent gene, PDX1, which
encodes for a key β cell transcription factor. Importantly, this was observed for both
the mouse and human orthologs, and similar effects were obtained through RNAi
suppression or through CRISPR–induced transcriptional interference of PLUTO. Our
studies further showed that PLUTO promotes 3D interactions between the PDX1
promoter and its upstream enhancer cluster, which is contained within the body of
the PLUTO gene. We thus propose that PLUTO regulates the 3D architecture of the
enhancer cluster at the PDX1 locus. This finding is reminiscent, yet distinct from
earlier examples of non-coding RNA genes that modulate 3D chromosomal structure
(Lai et al., 2013; Yao et al., 2010). Given that a significant number of lncRNAs are
co-expressed with adjacent lineage-specific protein-coding genes, it is possible that
17
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
the general regulatory paradigm described here is relevant to analogous lncRNAprotein coding gene pairs.
Taken together, our data implicate cell-specific lncRNAs in human β cell
transcriptional programs. Given the importance of TFs in the pathophysiology of
human diabetes and their role in β cell programming strategies, it now seems
reasonable to explore whether β cell lncRNAs also play analogous roles (Bell and
Polonsky, 2001; Flanagan et al., 2014; Zhou et al., 2008). The findings reported here
therefore strengthen earlier suggestions that defects in β cell lncRNAs might
contribute to the pathogenesis of human diabetes (Fadista et al., 2014; Moran et al.,
2012), and warrant an assessment of whether they can be harnessed to promote β
cell differentiation, function or cellular mass.
18
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Experimental procedures.
Pancreatic Islets
Human islets used for RNA-seq and ChIP-seq were cultured with CMRL 1066
medium containing 10% Fetal Calf Serum (FCS) before shipment, after which they
were cultured for three days with RPMI 1640 medium containing 11 mM glucose,
supplemented with 10% FCS.
Glucose stimulated insulin release
Glucose stimulated insulin release was assayed in EndoC-βH1 or EndoC-βH3 cells
as described (Benzara et al., 2015, Ravassard et al., 2011).
RNA analysis
RNA was isolated with Tripure (Roche) and treated with DNase I (Sigma). qPCR was
performed with SYBR green or Taqman probe detection (van Arensbergen et al.,
2010). See Table S4 for oligonucleotide and probe sequences.
amiRNA and CRISPRi experiments
Lentiviral vectors carrying amiRNAs targeting TFs, lncRNAs and non-targeting
control sequences were transduced into the EndoC-βH1 human β cell line as
described (Castaing et al., 2005; Ravassard et al., 2011; Scharfmann et al., 2014).
Figure S1A illustrates the vector design. Oligonucleotide sequences are shown in
Table S4. Non-transduced cells were assayed in parallel. Cells were harvested at 80
hours post transduction for RNA extraction. For transduction of human islets, islets
were first dispersed using trypsin-EDTA and gentle agitation. CRISPRi experiments
19
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
were performed with two gRNAs designed to target PLUTO exon 1, or two unrelated
intergenic control regions, and transfected in EndoC-βH3 cells (Table S4).
Gene expression array analysis
RNA was hybridized onto HTA2.0 Affymetrix arrays. RMA normalization was carried
out using Expression Console (Affymetrix). Gene based differential expression
analysis was done using Transcriptome Analysis Console (TAC, Affymetrix).
Enhancer cluster genes were defined by genes that were associated with clustered
islet enhancers that show top 50 percentile binding by TFs (PDX1, FOXA2, NKX2-2,
NKX6.1, MAFB), as defined previously (Pasquali et al., 2014). Pancreatic islet gene
sets used for enrichment analysis are shown in Table S5. A list of islet-enriched
genes was generated as those with more than two standard deviations higher
expression in human islets than the average expression in 16 human tissues (Table
S5). Data (cel and chp files) can be found at Gene Expression Omnibus (GEO,
accession: GSE83619).
Differential expression in IGT and T2D islets.
RNA-seq data has been previously described (Fadista et al., 2014). The samples
were aligned to the hg19 genome using STAR aligner version 2.3.0 as described in
supplemental methods, quantification was carried out with HTseq-Count 0.6.1, and
differential expression analysis of lncRNA genes was done using DEseq2 1.10
(Table S3), using an adjusted p-value threshold of 0.05.
Chromatin conformation capture (3C)
20
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
3C and 4C-seq was carried out as previously described (Pasquali et al., 2014; Tena
et al., 2011) For real-time PCR quantification, readings were normalized to a control
region within the PDX1 intron. Normalized values are expressed as a fraction of nontargeting amiRNA control sample. See Table S4 for oligonucleotide sequences.
Annotation of islet lncRNAs.
LncRNAs were annotated through de novo assembly of ~5 billion stranded pairedend RNA-seq reads from 41 human islet samples, filtered for expression in FACSpurified β cell cells, lack of enrichment in the pancreatic exocrine fraction to exclude
acinar contaminants, and presence of presence of H3K4me3 enrichment in the
vicinity of the 5’ end. A more detailed description of the annotation process is
provided in supplemental methods. Annotations are available in Table S3 and can
be accessed on a UCSC genome browser (GRCh37/hg19) session by selecting
“track hubs”, and selecting “Human Islet lncRNAs”. Alternatively the track hub can
be directly visualized in the UCSC Genome Browser.
Network analysis
WGCNA(v2) tool was used to build a co-transcriptional network based on mRNAs
from 64 human islet RNA-seq samples.
Author contributions
J.F. and I.A. conceived the idea, designed experiments and wrote the
manuscript. J.F. supervised and I.A. coordinated the project. I.A., Z.T., H.W., J.Y.,
C.A., E.S., A.S., L. Pasquali and D.M.Y.R. contributed to data analysis. I.A., A.B.,
M.B., C.S.C., R.G.F., J.G.H. and N.C. performed experiments. D.M.Y.R, I.M. and
21
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
N.N. annotated lncRNAs. L.Piemonti, T.B., C.B., J.K.C., F.P. provided samples. I.A.,
J.F., Z.T., A.B., D.M.Y.R, L.G., C.B., J.K.C., F.P., P.R., A.S., L.G., C.A., E.S.
discussed results. All authors read and approved the manuscript. Z.T, A.B., D.M.Y.R,
C.S-C. contributed equally.
Acknowledgements
This research was supported by the National Institute for Health Research (NIHR)
Imperial Biomedical Research Centre. Work was funded by grants from the
Wellcome Trust (WT101033 to J.F.), NIH-BCBC (2U01 DK072473-06 to J.F., P.R)
Ministerio de Economía y Competitividad (BFU2014-54284-R to J.F.) and Horizon
2020 (667191 to J.F.). Work in IDIBAPS was supported by the CERCA Programme,
Generalitat de Catalunya. J.Y. was supported through Berg and Unity Biotechnology
fellowship. The authors are grateful to Helena Raurell Vila for experimental help and
Romain Derelle and Loris Mularoni for advice in bioinformatic analysis. P. R. is a
shareholder and consultant for Endocells/Unicercell Biosolutions. Z.T. receives
financial support from Berg Pharma and Unity Biotechnology as a consultant.
References
Ahlgren,U.,Jonsson,J.,Jonsson,L.,Simu,K.,andEdlund,H.(1998).beta-cell-specificinactivationof
themouseIpf1/Pdx1generesultsinlossofthebeta-cellphenotypeandmaturityonsetdiabetes.
Genes&development12,1763-1768.
Anderson,K.R.,Singer,R.A.,Balderes,D.A.,Hernandez-Lagunas,L.,Johnson,C.W.,Artinger,K.B.,and
Sussel,L.(2011).TheL6domaintetraspaninTm4sf4regulatesendocrinepancreasdifferentiation
anddirectedcellmigration.Development138,3213-3224.
22
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Andrews,S.J.,andRothnagel,J.A.(2014).Emergingevidenceforfunctionalpeptidesencodedby
shortopenreadingframes.Naturereviews.Genetics15,193-204.
Bell,G.I.,andPolonsky,K.S.(2001).Diabetesmellitusandgeneticallyprogrammeddefectsinbetacellfunction.Nature414,788-791.
Benner,C.,vanderMeulen,T.,Caceres,E.,Tigyi,K.,Donaldson,C.J.,andHuising,M.O.(2014).The
transcriptionallandscapeofmousebetacellscomparedtohumanbetacellsrevealsnotablespecies
differencesinlongnon-codingRNAandprotein-codinggeneexpression.BMCgenomics15,620.
Benazra,M.,Lecomte,M.J.,Colace,C.,Muller,A.,Machado,C.,Pechberty,S.,Bricout-Neveu,E.,
Grenier-Godard,M.,Solimena,M.,Scharfmann,R.,etal.(2015).Ahumanbetacelllinewithdrug
inducibleexcisionofimmortalizingtransgenes.Molecularmetabolism4,916-925.
Cabili,M.N.,Trapnell,C.,Goff,L.,Koziol,M.,Tazon-Vega,B.,Regev,A.,andRinn,J.L.(2011).
IntegrativeannotationofhumanlargeintergenicnoncodingRNAsrevealsglobalpropertiesand
specificsubclasses.Genes&development25,1915-1927.
Carninci,P.,Kasukawa,T.,Katayama,S.,Gough,J.,Frith,M.C.,Maeda,N.,Oyama,R.,Ravasi,T.,
Lenhard,B.,Wells,C.,etal.(2005).Thetranscriptionallandscapeofthemammaliangenome.
Science309,1559-1563.
Carrieri,C.,Cimatti,L.,Biagioli,M.,Beugnet,A.,Zucchelli,S.,Fedele,S.,Pesce,E.,Ferrer,I.,Collavin,
L.,Santoro,C.,etal.(2012).Longnon-codingantisenseRNAcontrolsUchl1translationthroughan
embeddedSINEB2repeat.Nature491,454-457.
Castaing,M.,Guerci,A.,Mallet,J.,Czernichow,P.,Ravassard,P.,andScharfmann,R.(2005).Efficient
restrictedgeneexpressioninbetacellsbylentivirus-mediatedgenetransferintopancreatic
stem/progenitorcells.Diabetologia48,709-719.
23
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Chen,L.L.,andCarmichael,G.G.(2009).AlterednuclearretentionofmRNAscontaininginverted
repeatsinhumanembryonicstemcells:functionalroleofanuclearnoncodingRNA.Molecularcell
35,467-478.
Derrien,T.,Johnson,R.,Bussotti,G.,Tanzer,A.,Djebali,S.,Tilgner,H.,Guernec,G.,Martin,D.,
Merkel,A.,Knowles,D.G.,etal.(2012).TheGENCODEv7catalogofhumanlongnoncodingRNAs:
analysisoftheirgenestructure,evolution,andexpression.Genomeresearch22,1775-1789.
Derry,J.M.,Zhong,H.,Molony,C.,MacNeil,D.,Guhathakurta,D.,Zhang,B.,Mudgett,J.,Small,K.,El
Fertak,L.,Guimond,A.,etal.(2010).Identificationofgenesandnetworksdrivingcardiovascularand
metabolicphenotypesinamouseF2intercross.PloSone5,e14319.
Fadista,J.,Vikman,P.,Laakso,E.O.,Mollet,I.G.,Esguerra,J.L.,Taneera,J.,Storm,P.,Osmark,P.,
Ladenvall,C.,Prasad,R.B.,etal.(2014).Globalgenomicandtranscriptomicanalysisofhuman
pancreaticisletsrevealsnovelgenesinfluencingglucosemetabolism.ProceedingsoftheNational
AcademyofSciencesoftheUnitedStatesofAmerica111,13924-13929.
Flanagan,S.E.,DeFranco,E.,LangoAllen,H.,Zerah,M.,Abdul-Rasoul,M.M.,Edge,J.A.,Stewart,H.,
Alamiri,E.,Hussain,K.,Wallis,S.,etal.(2014).Analysisoftranscriptionfactorskeyformouse
pancreaticdevelopmentestablishesNKX2-2andMNX1mutationsascausesofneonataldiabetesin
man.Cellmetabolism19,146-154.
Goff,L.A.,Groff,A.F.,Sauvageau,M.,Trayes-Gibson,Z.,Sanchez-Gomez,D.B.,Morse,M.,Martin,
R.D.,Elcavage,L.E.,Liapis,S.C.,Gonzalez-Celeiro,M.,etal.(2015).Spatiotemporalexpressionand
transcriptionalperturbationsbylongnoncodingRNAsinthemousebrain.Proceedingsofthe
NationalAcademyofSciencesoftheUnitedStatesofAmerica112,6855-6862.
Gong,C.,andMaquat,L.E.(2011).lncRNAstransactivateSTAU1-mediatedmRNAdecaybyduplexing
with3'UTRsviaAluelements.Nature470,284-288.
24
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Guttman,M.,Amit,I.,Garber,M.,French,C.,Lin,M.F.,Feldser,D.,Huarte,M.,Zuk,O.,Carey,B.W.,
Cassady,J.P.,etal.(2009).ChromatinsignaturerevealsoverathousandhighlyconservedlargenoncodingRNAsinmammals.Nature458,223-227.
Guttman,M.,Donaghey,J.,Carey,B.W.,Garber,M.,Grenier,J.K.,Munson,G.,Young,G.,Lucas,A.B.,
Ach,R.,Bruhn,L.,etal.(2011).lincRNAsactinthecircuitrycontrollingpluripotencyand
differentiation.Nature477,295-300.
Huarte,M.,Guttman,M.,Feldser,D.,Garber,M.,Koziol,M.J.,Kenzelmann-Broz,D.,Khalil,A.M.,Zuk,
O.,Amit,I.,Rabani,M.,etal.(2010).AlargeintergenicnoncodingRNAinducedbyp53mediates
globalgenerepressioninthep53response.Cell142,409-419.
Hung,T.,Wang,Y.,Lin,M.F.,Koegel,A.K.,Kotake,Y.,Grant,G.D.,Horlings,H.M.,Shah,N.,Umbricht,
C.,Wang,P.,etal.(2011).ExtensiveandcoordinatedtranscriptionofnoncodingRNAswithincellcyclepromoters.Naturegenetics43,621-629.
Iyer,M.K.,Niknafs,Y.S.,Malik,R.,Singhal,U.,Sahu,A.,Hosono,Y.,Barrette,T.R.,Prensner,J.R.,
Evans,J.R.,Zhao,S.,etal.(2015).ThelandscapeoflongnoncodingRNAsinthehuman
transcriptome.Naturegenetics47,199-208.
Jonsson,J.,Carlsson,L.,Edlund,T.,andEdlund,H.(1994).Insulin-promoter-factor1isrequiredfor
pancreasdevelopmentinmice.Nature371,606-609.
Kim,S.K.,Lund,J.,Kiraly,M.,Duke,K.,Jiang,M.,Stuart,J.M.,Eizinger,A.,Wylie,B.N.,andDavidson,
G.S.(2001).AgeneexpressionmapforCaenorhabditiselegans.Science293,2087-2092.
Klattenhoff,C.A.,Scheuermann,J.C.,Surface,L.E.,Bradley,R.K.,Fields,P.A.,Steinhauser,M.L.,Ding,
H.,Butty,V.L.,Torrey,L.,Haas,S.,etal.(2013).Braveheart,alongnoncodingRNArequiredfor
cardiovascularlineagecommitment.Cell152,570-583.
25
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Kretz,M.,Siprashvili,Z.,Chu,C.,Webster,D.E.,Zehnder,A.,Qu,K.,Lee,C.S.,Flockhart,R.J.,Groff,
A.F.,Chow,J.,etal.(2013).Controlofsomatictissuedifferentiationbythelongnon-codingRNA
TINCR.Nature493,231-235.
Ku,G.M.,Kim,H.,Vaughn,I.W.,Hangauer,M.J.,MyungOh,C.,German,M.S.,andMcManus,M.T.
(2012).Researchresource:RNA-Seqrevealsuniquefeaturesofthepancreaticbeta-cell
transcriptome.Molecularendocrinology26,1783-1792.
Lai,F.,Orom,U.A.,Cesaroni,M.,Beringer,M.,Taatjes,D.J.,Blobel,G.A.,andShiekhattar,R.(2013).
ActivatingRNAsassociatewithMediatortoenhancechromatinarchitectureandtranscription.
Nature494,497-501.
Li,C.,Chen,P.,Palladino,A.,Narayan,S.,Russell,L.K.,Sayed,S.,Xiong,G.,Chen,J.,Stokes,D.,Butt,
Y.M.,etal.(2010).Mechanismofhyperinsulinisminshort-chain3-hydroxyacyl-CoAdehydrogenase
deficiencyinvolvesactivationofglutamatedehydrogenase.TheJournalofbiologicalchemistry285,
31806-31818.
Louagie,E.,Taylor,N.A.,Flamez,D.,Roebroek,A.J.,Bright,N.A.,Meulemans,S.,Quintens,R.,
Herrera,P.L.,Schuit,F.,VandeVen,W.J.,etal.(2008).Roleoffuriningranularacidificationinthe
endocrinepancreas:identificationoftheV-ATPasesubunitAc45asacandidatesubstrate.
ProceedingsoftheNationalAcademyofSciencesoftheUnitedStatesofAmerica105,12319-12324.
Luco,R.F.,andMisteli,T.(2011).Morethanasplicingcode:integratingtheroleofRNA,chromatin
andnon-codingRNAinalternativesplicingregulation.Currentopinioningenetics&development
21,366-372.
Moran,I.,Akerman,I.,vandeBunt,M.,Xie,R.,Benazra,M.,Nammo,T.,Arnes,L.,Nakic,N.,GarciaHurtado,J.,Rodriguez-Segui,S.,etal.(2012).Humanbetacelltranscriptomeanalysisuncovers
lncRNAsthataretissue-specific,dynamicallyregulated,andabnormallyexpressedintype2diabetes.
Cellmetabolism16,435-448.
26
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Offield,M.F.,Jetton,T.L.,Labosky,P.A.,Ray,M.,Stein,R.W.,Magnuson,M.A.,Hogan,B.L.,and
Wright,C.V.(1996).PDX-1isrequiredforpancreaticoutgrowthanddifferentiationoftherostral
duodenum.Development122,983-995.
Okamoto,K.,Iwasaki,N.,Doi,K.,Noiri,E.,Iwamoto,Y.,Uchigata,Y.,Fujita,T.,andTokunaga,K.
(2012).Inhibitionofglucose-stimulatedinsulinsecretionbyKCNJ15,anewlyidentifiedsusceptibility
genefortype2diabetes.Diabetes61,1734-1741.
Okazaki,Y.,Furuno,M.,Kasukawa,T.,Adachi,J.,Bono,H.,Kondo,S.,Nikaido,I.,Osato,N.,Saito,R.,
Suzuki,H.,etal.(2002).Analysisofthemousetranscriptomebasedonfunctionalannotationof
60,770full-lengthcDNAs.Nature420,563-573.
Pandey,G.,Zhang,B.,Chang,A.N.,Myers,C.L.,Zhu,J.,Kumar,V.,andSchadt,E.E.(2010).An
integrativemulti-networkandmulti-classifierapproachtopredictgeneticinteractions.PLoS
computationalbiology6.
Pang,K.C.,Frith,M.C.,andMattick,J.S.(2006).RapidevolutionofnoncodingRNAs:lackof
conservationdoesnotmeanlackoffunction.Trendsingenetics:TIG22,1-5.
Pasquali,L.,Gaulton,K.J.,Rodriguez-Segui,S.A.,Mularoni,L.,Miguel-Escalada,I.,Akerman,I.,Tena,
J.J.,Moran,I.,Gomez-Marin,C.,vandeBunt,M.,etal.(2014).Pancreaticisletenhancerclusters
enrichedintype2diabetesrisk-associatedvariants.Naturegenetics46,136-143.
Pauli,A.,Valen,E.,Lin,M.F.,Garber,M.,Vastenhouw,N.L.,Levin,J.Z.,Fan,L.,Sandelin,A.,Rinn,J.L.,
Regev,A.,etal.(2012).SystematicidentificationoflongnoncodingRNAsexpressedduringzebrafish
embryogenesis.Genomeresearch22,577-591.
Penny,G.D.,Kay,G.F.,Sheardown,S.A.,Rastan,S.,andBrockdorff,N.(1996).RequirementforXistin
Xchromosomeinactivation.Nature379,131-137.
Pott,S.,andLieb,J.D.(2015).Whataresuper-enhancers?Naturegenetics47,8-12.
27
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Qiu,Y.,Guo,M.,Huang,S.,andStein,R.(2002).Insulingenetranscriptionismediatedby
interactionsbetweenthep300coactivatorandPDX-1,BETA2,andE47.Molecularandcellular
biology22,412-420.
Ravassard,P.,Hazhouz,Y.,Pechberty,S.,Bricout-Neveu,E.,Armanet,M.,Czernichow,P.,and
Scharfmann,R.(2011).Ageneticallyengineeredhumanpancreaticbetacelllineexhibitingglucoseinducibleinsulinsecretion.TheJournalofclinicalinvestigation121,3589-3597.
Rinn,J.L.,andChang,H.Y.(2012).GenomeregulationbylongnoncodingRNAs.Annualreviewof
biochemistry81,145-166.
Scharfmann,R.,Pechberty,S.,Hazhouz,Y.,vonBulow,M.,Bricout-Neveu,E.,Grenier-Godard,M.,
Guez,F.,Rachdi,L.,Lohmann,M.,Czernichow,P.,etal.(2014).Developmentofaconditionally
immortalizedhumanpancreaticbetacellline.TheJournalofclinicalinvestigation124,2087-2098.
Schmitt,A.M.,andChang,H.Y.(2013).Generegulation:LongRNAswireupcancergrowth.Nature
500,536-537.
Segal,E.,Shapira,M.,Regev,A.,Pe'er,D.,Botstein,D.,Koller,D.,andFriedman,N.(2003).Module
networks:identifyingregulatorymodulesandtheircondition-specificregulatorsfromgene
expressiondata.Naturegenetics34,166-176.
Sleutels,F.,Zwart,R.,andBarlow,D.P.(2002).Thenon-codingAirRNAisrequiredforsilencing
autosomalimprintedgenes.Nature415,810-813.
Smith,S.B.,Qu,H.Q.,Taleb,N.,Kishimoto,N.Y.,Scheel,D.W.,Lu,Y.,Patch,A.M.,Grabs,R.,Wang,J.,
Lynn,F.C.,etal.(2010).Rfx6directsisletformationandinsulinproductioninmiceandhumans.
Nature463,775-780.
28
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Stoffers,D.A.,Zinkin,N.T.,Stanojevic,V.,Clarke,W.L.,andHabener,J.F.(1997).Pancreaticagenesis
attributabletoasinglenucleotidedeletioninthehumanIPF1genecodingsequence.Nature
genetics15,106-110.
Stuart,J.M.,Segal,E.,Koller,D.,andKim,S.K.(2003).Agene-coexpressionnetworkforglobal
discoveryofconservedgeneticmodules.Science302,249-255.
Su,W.L.,Kleinhanz,R.R.,andSchadt,E.E.(2011).CharacterizingtheroleofmiRNAswithingene
regulatorynetworksusingintegrativegenomicstechniques.Molecularsystemsbiology7,490.
Tena,J.J.,Alonso,M.E.,delaCalle-Mustienes,E.,Splinter,E.,deLaat,W.,Manzanares,M.,and
Gomez-Skarmeta,J.L.(2011).Anevolutionarilyconservedthree-dimensionalstructureinthe
vertebrateIrxclustersfacilitatesenhancersharingandcoregulation.Naturecommunications2,310.
Tian,G.,Sagetorp,J.,Xu,Y.,Shuai,H.,Degerman,E.,andTengholm,A.(2012).Roleof
phosphodiesterasesintheshapingofsub-plasma-membranecAMPoscillationsandpulsatileinsulin
secretion.Journalofcellscience125,5084-5095.
Ulitsky,I.,Shkumatava,A.,Jan,C.H.,Sive,H.,andBartel,D.P.(2011).ConservedfunctionoflincRNAs
invertebrateembryonicdevelopmentdespiterapidsequenceevolution.Cell147,1537-1550.
vanArensbergen,J.,Garcia-Hurtado,J.,Moran,I.,Maestro,M.A.,Xu,X.,VandeCasteele,M.,
Skoudy,A.L.,Palassini,M.,Heimberg,H.,andFerrer,J.(2010).DerepressionofPolycombtargets
duringpancreaticorganogenesisallowsinsulin-producingbeta-cellstoadoptaneuralgeneactivity
program.Genomeresearch20,722-732.
Varadi,A.,andRutter,G.A.(2002).DynamicimagingofendoplasmicreticulumCa2+concentrationin
insulin-secretingMIN6Cellsusingrecombinanttargetedcameleons:rolesofsarco(endo)plasmic
reticulumCa2+-ATPase(SERCA)-2andryanodinereceptors.Diabetes51Suppl1,S190-201.
29
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Wagner,T.F.,Loch,S.,Lambert,S.,Straub,I.,Mannebach,S.,Mathar,I.,Dufer,M.,Lis,A.,Flockerzi,
V.,Philipp,S.E.,etal.(2008).TransientreceptorpotentialM3channelsareionotropicsteroid
receptorsinpancreaticbetacells.Naturecellbiology10,1421-1430.
Wang,K.C.,andChang,H.Y.(2011).MolecularmechanismsoflongnoncodingRNAs.Molecularcell
43,904-914.
Willingham,A.T.,Orth,A.P.,Batalov,S.,Peters,E.C.,Wen,B.G.,Aza-Blanc,P.,Hogenesch,J.B.,and
Schultz,P.G.(2005).AstrategyforprobingthefunctionofnoncodingRNAsfindsarepressorof
NFAT.Science309,1570-1573.
Wilson,M.E.,Scheel,D.,andGerman,M.S.(2003).Geneexpressioncascadesinpancreatic
development.Mechanismsofdevelopment120,65-80.
Yang,Y.H.,ManningFox,J.E.,Zhang,K.L.,MacDonald,P.E.,andJohnson,J.D.(2013).IntraisletSLITROBOsignalingisrequiredforbeta-cellsurvivalandpotentiatesinsulinsecretion.Proceedingsofthe
NationalAcademyofSciencesoftheUnitedStatesofAmerica110,16480-16485.
Yao,H.,Brick,K.,Evrard,Y.,Xiao,T.,Camerini-Otero,R.D.,andFelsenfeld,G.(2010).Mediationof
CTCFtranscriptionalinsulationbyDEAD-boxRNA-bindingproteinp68andsteroidreceptorRNA
activatorSRA.Genes&development24,2543-2555.
Zhou,Q.,Brown,J.,Kanarek,A.,Rajagopal,J.,andMelton,D.A.(2008).Invivoreprogrammingof
adultpancreaticexocrinecellstobeta-cells.Nature455,627-632.
Zito,E.,Chin,K.T.,Blais,J.,Harding,H.P.,andRon,D.(2010).ERO1-beta,apancreas-specificdisulfide
oxidase,promotesinsulinbiogenesisandglucosehomeostasis.TheJournalofcellbiology188,821832.
30
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Figure 1. Knockdown of selected β cell lncRNAs leads to transcriptional
phenotypes.
(A) Schematic representation of the experimental plan. Lentiviral encoded amiRNAs
were validated and transduced in duplicate (x 2) or triplicate (x 3) into ENDOC-βH1
cells as indicated, and then analyzed with oligonucleotide expression arrays. (B)
Differential gene expression analysis revealed genes that show significant up or
downregulation after knockdown of TFs or lncRNAs. For each TF or lncRNA, we
combined all replicates transduced with the different target-specific amiRNAs, and
compared these to all replicates from 5 non-targeting controls. Differential
expression was determined at p<10-3 (ANOVA). (C) We compared gene expression
data from all 10 possible combinations of 3 vs. 2 control non-targeting amiRNAs.
Similarly, the two independent amiRNAs that target each TF or lncRNA were
compared to all 10 possible combinations of 3 control amiRNAs. For this analysis we
only considered the 7 lncRNAs that were targeted by two independent amiRNAs. (D)
Control comparisons result in a low number of differentially regulated genes
(average 15 genes), while most TF and lncRNA comparisons yield higher numbers
of differentially regulated genes. ***p<10-4, **p<0.01, ns: not significant, as compared
to control comparisons, Mann-Whitney test. (E) HI-LNC15 regulates its neighboring
gene NKX2.2, while HI-LNC12 knockdown (KD) does not affect its adjacent active
gene, UNC5A (left panel). Further examples are shown in Figure S1G. RNAs were
normalized to TBP mRNA and expressed relative to control amiRNAs; n=3, error
bars represent SEM, **p<0.01, *p<0.05 (Students t-test).
Figure 2. Knockdown of lncRNAs impairs insulin secretion. (A) Examples of
genes known to play a role in β cell function regulated by islet lncRNAs. (B) Glucose-
31
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
stimulated insulin secretion was tested on T-antigen excised EndoC-βH3 cells after
transduction with amiRNAs targeting indicated lncRNAs or controls. Secreted or total
insulin content was normalized to the number of cells per well and expressed as fold
change over control amiRNA treatment at 2.8 mM glucose. Each bar represents an
average from two independent amiRNA vectors and 12 separate wells, from two
independent experiments. Error bars represent SEM, *** p<10-3, ** p<0.01, *p<0.05
(Student’s t-test).
Figure 3. Human islet TFs and lncRNAs regulate common genes
(A) Heatmap displaying Pearson r values for all pairwise comparisons of foldchanges in gene expression after knockdown of TFs and lncRNAs. Only genes
significantly dysregulated at p<10-3 in at least one condition were included in the
analysis. (B) Unsupervised clustering analysis of fold-change values after
knockdown of 5 TFs and the 5 lncRNAs that displayed the strongest transcriptional
changes. Only genes that were dysregulated at p<10-3 in at least one knockdown
were selected. Blue represents downregulated and red represents upregulated
genes. Controls represent control comparisons as described for Figure 1. (C)
Examples of highly correlated transcriptional phenotypes. The plots show foldchange values (Log2) after knockdown of indicated pairs of genes. Only the top 100
most regulated genes for any of the two knockdowns were plotted. Pearson´s
correlation (r) and p-values are displayed.
Figure 4. LncRNAs regulate enhancer cluster genes. Gene Set Enrichment
analysis (GSEA) showed that genes that were downregulated upon knockdown of
32
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
either islet TFs or lncRNAs were enriched in a set of 694 genes that is associated
with human islet enhancer clusters (red dots), but not in 10 control gene sets (black
dots) that were expressed at similar levels as enhancer cluster genes.
Figure 5. Islet-specific coding and noncoding RNAs form shared coexpression modules. (A) Topological overlap matrix representing co-expression
modules that were co-regulated across 64 human islet samples. Modules that were
enriched in lncRNAs are marked with squares (hypergeometric test, p<10-2). (B-D)
Co-expression modules that showed enrichment in (B) islet lncRNAs, (C) islet
enhancer cluster (EC)-associated genes, or (D) a set of 94 islet-enriched TF genes.
Five modules (M3, M7, M12, M18 and M20, marked in blue) out of seven modules
that were enriched in lncRNAs were also enriched in ECs and TFs. (E) Module M3
was enriched in typical islet-specific biological process annotations. The right panel
shows examples of islet TFs and lncRNAs in module M3. (F) Correlation of indicated
lncRNAs and β cell-specific TF mRNAs across 64 islet samples. GAPDH is shown
as a non β cell reference. Pearson´s correlation values are displayed in the top left
corner. The axes show expression values normalized across 64 islet samples. (G)
Network diagram illustrating that TFs and lncRNAs often co-regulate the same
genes, many of which were associated with enhancer clusters.
Figure 6. PLUTO knockdown decreases PDX1 mRNA. (A) Downregulation of
PLUTO (HI-LNC71) and PDX1 in islets from donors with T2D or IGT. Differential
expression analysis was performed on control (n=50) versus T2D (n=10) or IGT
(n=15) samples. Boxplots represent expression normalized to mean of control
33
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
samples. Adjusted p-values are shown. (B) Schematic representation of the human
PDX1 locus and its associated enhancer cluster. 4C-seq analysis was designed to
identify regions interacting with the PDX1 promoter region in EndoC-βH1 cells. Red
and orange vertical lines depict active and poised islet enhancers, respectively. F
and R represent forward and reverse RNA-seq strands, scales represent RPM.
PLUTO (HI-LNC71) was generated from a de novo assembly of islet RNA-seq, and
differs from a transcript annotated in UCSC and RefSeq that originates from a PDX1
intronic region. (C) Downregulation of PLUTO or PDX1 using amiRNAs resulted in
reduced PDX1 mRNA and protein levels. EndoC-βH1 cells were transduced with
control (black), PLUTO (white) or PDX1 (turquoise) amiRNA vectors 80 hours prior
to harvest. RNA levels were assessed by qPCR, normalized to TBP and expressed
as fold over control amiRNA samples (n=4). For protein quantification, PDX1 levels
were first normalized to the average of TBP and H3 levels and then compared to the
control amiRNA sample. (D) Downregulation of PLUTO in human islet cells results in
reduced PDX1 mRNA levels. Islet cells were dispersed and transduced with amiRNA
vectors (n=3) as in (B). (E) Downregulation of PLUTO in EndoC-βH3 cells using
CRISPRi also decreases PDX1 mRNA. EndoC-βH3 cells were nucleofected with
CRISPRi vectors 80 hours prior to harvest. RNA levels were assessed by qPCR,
normalized to TBP and then to control CRISPRi sample (n=3). (F) PDX1 and PLUTO
RNA levels were highly correlated in 64 human islet samples. (G) Knockdown of
PDX1 and PLUTO resulted in differential expression of similar genes. Fold change
value (Log2) of top 250 dysregulated genes following the PDX1 knockdown was
plotted against the same genes following the PLUTO knockdown. (H) Gene Set
Enrichment analysis (GSEA) showed that genes that were downregulated upon
knockdown of PDX1 and PLUTO were enriched in genes whose enhancers were
34
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
bound by PDX1 (red) in islets, but not in 10 control gene sets (black) that were
expressed at similar levels as PDX1-bound genes. (I) Knockdown of PDX1 and
PLUTO resulted in differential expression of genes with similar biological process
annotations. (J) Examples of known PDX1 regulated genes that are also coregulated by PLUTO in parallel knockdown experiments. mRNA levels were
assessed as in (B). Error bars denote SEM, *** p<10-3, **p<0.01, *p<0.05 (Student’s
t test).
Figure 7. PLUTO regulates PDX1 transcription and 3D chromatin structure
(A) The mRNA stability of PDX1 was unaffected by PLUTO knockdown. PDX1
mRNA was measured in control and PLUTO amiRNA knockdown in EndoC-βH1
cells after Actinomycin D (ActD) treatment (n=3). mRNA levels are presented as a
percentage of levels observed at time=0. (B) Knockdown of PLUTO was carried out
as in Figure 6B, and this led to reduced PDX1 transcription as assessed by qPCR
analysis of intronic PDX1 RNA levels using hydrolysis probes. Values were
normalized to TBP mRNA and expressed as fold over control amiRNA sample (n=4).
(C) Schematic of selected epigenomic features of the PDX1 locus, (D) PLUTO is
required for 3D contacts between the PDX1 promoter and distal enhancers. 3C
analysis revealed that knockdown of PLUTO resulted in reduced contacts between
PDX1 promoter (anchor) and two enhancers (E1,E2). Interaction signals were
normalized to a control region on PDX1 intron. CTL represents a negative control
region that does not harbor interactions with the PDX1 promoter. Error bars denote
±SEM, p values are from a Student’s t test. (E) PLUTO knockdown resulted in
impaired 3D contacts between the PDX1 promoter and its adjacent enhancer cluster,
causing reduced PDX1 transcriptional activity.
35
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
C4 C5
vs.
Combination 2
Combination 2
C1 C2 C4
sh1 sh2
C1 C2 C3
vs.
C3 C5
C1 C2 C4
sh1 sh2
vs.
vs.
...
...
Combination 10
Combination 10
C3 C4 C5
C1 C2
C3 C4 C5
sh1 sh2
vs.
vs.
D
GLIS3
HNF1A
MAFB
NKX2.2
PDX1
HI-LNC12
HI-LNC15
HI-LNC30
HI-LNC75
HI-LNC76
HI-LNC78
HI-LNC80
HI-LNC25
HI-LNC70
HI-LNC71
HI-LNC79
HI-LNC85
600
600
Control vs
TF or HI-LNC
0.8
0.4
0
* **
Control amiRNA
HI-LNC15 amiRNA-1
HI-LNC15 amiRNA-2
***
******
***
0
V1
***
** ns
V2
V3
V4
V5
V6
V7
V8
V9
V10
V11
V12
V13
*
UNC5A mRNA
NKX2.2 mRNA
1.2
*** ***
***
300
Number of differentially expressed genes
E
***
***
Ctl vsCtl
GLIS3
HNF1A
MAFB
NKX2.2
PDX1
HI-LNC12
HI-LNC15
HI-LNC30
HI-LNC75
HI-LNC76
HI-LNC78
HI-LNC80
C1 C2 C3
-1000
Combination 1 HI-LNC12
Combination 1
-500
500
Control
vs. control
0
400
C
500
300
RNA harvest (80 hrs)
Affymetrix HTA2.0 analysis
Upregulated
Downregulated
200
Lentiviral transduction into
ENDOC-βH1 beta cells
1000
100
B
0
Validated amiRNAs:
- non-targeting controls (n=5, x2)
- TFs (n=5, two amiRNA/target, x2)
- lncRNAs (n=7, two amiRNA/target, x2)
- lncRNAs (n=5, one amiRNAi/target,x3)
Differentially expressed
genes from 10 combinations
A
Number of differentially
expressed genes
FIGURE 1
1.2
0.8
0.4
0
Control amiRNA
HI-LNC12 amiRNA-1
HI-LNC12 amiRNA-2
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
FIGURE 2
β-cell function genes regulated by lncRNAs
PGK1
PRKAR2A
RFX3
RFX6
ROBO1
SLC25A6
STAT3
TM4SF4
TMED10
Control KD
HI-LNC78 KD
*
*
15 mM +IBMX
1
15mM
1.5
2.8 mM +IBMX
0.5
**
*
**
2.8mM
*
15 mM +IBMX
15 mM
**
0
**
15 mM
**
2.8 mM +IBMX
*
0.5
*
0
0
15mM
15 mM +IBMX
1
5
2.8 mM
15 mM +IBMX
+IBMX
1.5
15
10
2.8mM
2.8 mM +IBMX
2.8mM
2.8
mM
0
15
0
*** *** ***
0.5
*
20
5
15 mM +IBMX
15mM
1
2.8 mM
1.5
15 mM
**
Control KD
HI-LNC71 KD
10
**
2.8mM 2.8 mM +IBMX
2.8 mM +IBMX
10
ERO1LB
HADH
KCNJ3
TM4SF4
PDX1
VAMP3
15mM
20
HI-LNC71
2.8 mM
***
30
0
Insulincontent
(foldovercontrol)
ADCY8
COG3
COPG2
CTNNB1
DOPEY1
EXOC4
HADH
KCNJ3
PDE8A
Control KD
HI-LNC12 KD
1515mM
mM
Secretedinsulin
(foldovercontrol)
B
KCNJ15
NFAT5
PAX6
PCSK2
PDE8A
ROBO1
ROBO2
SCIN
TM4SF4
TRPM3
1515mM
mM
ADCY8
ATP2A3
ATP6AP1
CACNA1A
CACNA1D
CADM1
CADPS
CREBBP
GNAS
HADH
HI-LNC78
2.8mM
HI-LNC12
2.8mM
2.8
mM
A
+IBMX
+IBMX
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
FIGURE 3
B
Pearson´s r value
0.5
GLIS3
HNF1A
MAFB
NKX2.2
PDX1
HI-LNC12
HI-LNC15
HI-LNC25
HI-LNC30
HI-LNC70
HI-LNC71
HI-LNC75
HI-LNC76
HI-LNC78
HI-LNC79
HI-LNC80
HI-LNC85
C
Upregulated
1
GLIS3
HNF1A
MAFB
NKX2.2
PDX1
HI-LNC12
HI-LNC15
HI-LNC25
HI-LNC30
HI-LNC70
HI-LNC71
HI-LNC75
HI-LNC76
HI-LNC78
HI-LNC79
HI-LNC80
HI-LNC85
0
Downregulated
HNF1A KD
(Log2 FC)
NKX2.2
GLIS3
MAFB
HNF1A
HI-LNC12
PDX1
HI-LNC15
HI-LNC78
HI-LNC71
HI-LNC80
Control_8
Control_2
Control_6
Control_3
Control_7
Control_10
Control_9
Control_1
Control_5
Control_4
A
MAFB KD
(Log2 FC)
Control KD
(Log2 FC)
HI-LNC78 KD
(Log2 FC)
r=0.87
p=10-71
r=0.89
p=10-79
NKX2.2 KD
(Log2 FC)
Control KD
(Log2 FC)
HI-LNC15 KD
(Log2 FC)
r=0.67
p=10-32
r=-0.1
p=0.08
r=-0.15
p=0.02
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Enhancer cluster genes
Control gene sets (n=10 )
3
2
p<0.05
1
0
Ctl vs Ctl
GLIS3
HNF1A
MAFB
NKX2.2
PDX1
HI-LNC12
HI-LNC15
HI-LNC30
HI-LNC75
HI-LNC76
HI-LNC78
HI-LNC80
HI-LNC25
HI-LNC70
HI-LNC71
HI-LNC79
HI-LNC85
GSEA FWER
p-value (-Log10)
FIGURE 4
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
FIGURE 5
A
M12
M21
M7
M20
M3
M18
B Islet lncRNAs
M13
M20
M7
M12
M3
M21
M18
30
M13
0
10 20
Enrichment
p-value (-log10)
D
E
Islet specific TFs
M3: Gene ontology terms
Ion transport
Synaptic transmission
Glucose homeostasis
Nervous system dev.
Secretion by cell
M3
M7
M18
M11
0
6
12
Enrichment
p-value (-log10)
NKX6-1 mRNA
r=0.65
HI-LNC78 RNA
r=-0.07
HI-LNC12 RNA
GAPDH mRNA
HI-LNC78 RNA
r=0.7
HI-LNC15 RNA
GAPDH mRNA
HI-LNC12 RNA
r=-0.07
r=0.71
HI-LNC80 RNA
PAX6 mRNA
r=0.78
GAPDH mRNA GAPDH mRNA
F
NKX6-1 mRNA
4
8
Enrichment
p-value (-log10)
PAX6 mRNA
0
r=0.08
HI-LNC80 RNA
r=-0.15
HI-LNC15 RNA
G
C
Islet enhancer
cluster genes
M3
M18
M20
M7
M12
0
20
40
Enrichment
p-value (-log10)
TFs and lncRNAs in M3
PDX1
NKX2.2
NKX6.1
MAFA
MAFB
PAX6
NEUROD1
HI-LNC12
HI-LNC15
HI-LNC71
HI-LNC80
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
A
p=0.008
22
Enhancer clusters
Enhancers
f2
ns
p=0.1
x
RNA levels
(normalised to control)
p=0.005
FIGURE 6
B
Control
IGT
T2D
p=0.07
33
CTL
EndoC-βH1
IGT
ns
T2D
11
4C-seq
70
Islet RNA-seq F
8
Islet RNA-seq R
PLUTO
00
0.4
PDX1 amiRNA
0
E
0
G
PLUTO KD
(Log2 FC)
r =0.86
p=10-15
0
10
20
PLUTO RNA (rpkm)
0
-1
1
PLUTO
dependent
genes
-1
0
H
0
r=0.79
p=10-54
Enrichment Score (-Log10p-value)
0
3
6
PDX1
dependent
genes
0.4
0
0
-1
******
0.4
1
Cellular localisation/Vesicle transport
Secretion by cell
Golgi vesicle-mediated transport
Lipid metabolic process
Steroid metabolic process
Protein localization/Protein transport
Cellular catabolic process
Protein localization/Vesicle transport
Golgi vesicle transport
Secretion
-1
J
1
0
3
2
1
0
r=0.03
p=0.65
Control
amiRNA
mRNA levels
PDX1 KD
(Log2 FC)
* **
0.8
Control KD
(Log2 FC)
1
40
0.8
PDX1 KD
PLUTO KD
0.4
1.2
PLUTO
amiRNA
PDX1
amiRNA
1.2
0.6
0
*
*
*
*
*
**
**
SORL1
0
0.8
1.2
SLC4A10
0.4
***
PDX1 mRNA
0.8
1.2
PDX1-bound
p-value (-Log10)
****
Control Crispri
PLUTO Crispri-1
PLUTO Crispri-2
SCD
0
PLUTO amiRNA
PLUTO RNA
1.2
80
0
I
0.4
Control amiRNA
0.8
Control amiRNA
PLUTO amiRNA
PLUTO RNA
Brightfield
Dispersed
human islet
GFP
F
0
0.8
1.2
IAPP
0.4
1.2
**
*
G6PC2
0.8
**
*
PDX1 mRNA
D
1.2
ns
*
PDX1 mRNA
PLUTO RNA
C
14
TBP
ERO1LB
f1
PDX1 protein
6
13
PLUTO
PDX1
PDX1 mRNA (rpkm)
!
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
FIGURE 7
Control amiRNA
PLUTO amiRNA
1
B
PDX1
intronic RNA
PDX1 mRNA
fraction remaining
A
0.5
0
0 0.5
1
2
4
p=0.002
1.2
Control amiRNA
0.8
PLUTO amiRNA
0.4
PDX1 amiRNA
0
Hours post ActD
C
CTCF
H3K27ac
PDX1
NKX2-2
FOXA2
PLUTO&
E1
CTL
D
E2
E
Control amiRNA
PLUTO amiRNA
Anchor
Enhancer
PLUTO
3C with PDX1 TSS
p=0.032
1.5
p=0.004
1
PDX1
PLUTO
knockdown
PDX1
0.5
0
PDX1 mRNA
CTL
E1
E2
PDX1 mRNA
bioRxiv preprint first posted online Dec. 23, 2016; doi: http://dx.doi.org/10.1101/096230. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
36